OK, when I said command line, this is exactly what your LDAP admin application will do, meaning applying "ldapmodify" command.
So you can do it using GUI through whatever application you want or command line, this is at then and from LDAP server standpoint exactly the same
If you can't find relevant topic here, then it means I was wrong and there is none. Apologies.
Then you just confirmed that my assumption is correct
: you are facing limitation due to the way Google Apps expect password to be stored.
So either you ask Google to support other password encryptions schemes or ask Zentyal to also support what Google expects but this aside, I doubt you will ever succeed.
I you where using Zentyal 2.2, you could achieve it as Zentyal stores different password schemes in different attributes.
With 3.0, I don't know but don't think so, at least in std LDAP container. I didn't check the Samba-LDAP one.
What I can however confirm is that both Zentyal 2.2 and 3.0 store at least one password in "userpassword" LDAP attribute.
I can't help further, sorry.
Either wait for Zentyal feedback or from someone having investigated this deeper.